Does this also prevent bookmarking between devices? If so, non-kindle .mobi files may just as well be converted to epub and placed in iBooks.

No, if you choose the send to Kindle option where your modified/custom book is sent to the Amazon cloud as a personal doc, then you can sync farthest page read, bookmarks, and highlights. I don't take notes on books so I'm not sure if notes will sync as well, but they probably do. Side loaded Kindle books are a different story.

EDIT: I typically set free my Amazon purchased books and ePubs that are purchased elsewhere, add an embedded font to make them easier to read, then send them to the Amazon cloud as personal docs. That way I can sync farthest page read, bookmarks, and highlights between the book on my iPad, Kindle Touch, and Fire HD. This works really well.